Molecular species identification of bushmeat recovered from the Serengeti ecosystem in Tanzania

Abstract

Bushmeat harvesting and consumption represents a potential risk for the spillover of endemic zoonotic pathogens, yet remains a common practice in many parts of the world. Given that the harvesting and selling of bushmeat is illegal in Tanzania and other parts of Africa, the supply chain is informal and may include hunters, whole-sellers, retailers, and individual resellers who typically sell bushmeat in small pieces. These pieces are often further processed, obscuring species-identifying morphological characteristics, contributing to incomplete or mistaken knowledge of species of origin and potentially confounding assessments of pathogen spillover risk and bushmeat offtake. The current investigation sought to identify the species of origin and assess the concordance between seller-reported and laboratory-confirmed species of origin of bushmeat harvested from in and around the Serengeti National Park in Tanzania. After obtaining necessary permits, the species of origin of a total of 151 bushmeat samples purchased from known intermediaries from 2016 to 2018 were characterized by PCR and sequence analysis of the cytochrome B (CytB) gene. Based on these sequence analyses, 30%, 95% Confidence Interval (CI: 24.4-38.6) of bushmeat samples were misidentified by sellers. Misreporting amongst the top five source species (wildebeest, buffalo, impala, zebra, and giraffe) ranged from 20% (CI: 11.4-33.2) for samples reported as wildebeest to 47% (CI: 22.2-72.7) for samples reported as zebra although there was no systematic bias in reporting. Our findings suggest that while misreporting errors are unlikely to confound wildlife offtake estimates for bushmeat consumption within the Serengeti ecosystem, the role of misreporting bias on the risk of spillover events of endemic zoonotic infections from bushmeat requires further investigation.

Fig 1. Sample distribution and metadata from selected samples collected in the Serengeti ecosystem.

A. The map shows the sites from where the 151 samples selected for molecular speciation were collected. The red dots represent the samples that speciated as the same species as reported (match), and the blue dots represent samples that did not match the reported species (mismatch). The number collected at each site is represented on the map with the percentage of mismatch samples. B. The proportion of samples collected from each different category is represented in the pie charts. The condition was either fresh (red, n = 91) or processed (blue, n = 60), the season was dry (red, n = 66) or rainy (blue, n = 85), whether the samples matched (red, n = 105) or mismatched (blue, n = 46) the reported species. The two pie charts on the bottom represent the reported species versus the species after speciation with the species represented by the legends associated with each pie.

Fig 2

A. Bar graph and heatmap showing the number of bushmeat samples reported for each species, and the discrepancy between reported and speciated species. Total counts of seller-reported species of origin are in the bar graphs. The points and lines represent correctly reported (matched—filled circles) and mismatched (open circles) counts of the speciation results. For each species, the heatmap shows the number of seller-reported species that were confirmed with laboratory characterization, and for those misidentified, shows the actual species of each laboratory-confirmed species as well as the International Union for Conservation of Nature (IUCN) Red List Categories for each species (N = 150). The x-axis represents the laboratory-confirmed species and the y-axis represents seller-reported species. Shown IUCN categories are least concern–LC; near threatened–NT; vulnerable–VU; not applicable—NA. B. The percent misreporting for the top five most abundant species. The table shows the top five most abundant species and the misreporting percentage with the 95% confidence interval (CI). The graph shows the percentage as the point and the 95% CI as the range. All confidence intervals overlap, so there is no difference in misreporting percentage among the different species demonstrating no systematic bias.

Fig 3. Proportions of the total collected species, seller-reported species, and laboratory confirmed species.

The table shows the total number of species from which samples were collected, reported, or speciated and the proportion of the total that each species represents (Reported n = 151, Laboratory-confirmed n = 151) and the 95% confidence interval. The plot is the graphical representation of the percentage (as a proportion) of each species (the point) and the 95% CI (range). The total collected species are shown in gray, the seller-reported species in black and the laboratory-confirmed species in red.